Claudio DiBacco

Demographic Responses of Estuarine Polychaetes to Pollutants: Life Table Response Experiments

Capitella sp. I and Streblospio benedicti are infaunal, deposit-feeding polychaetes that occur in estuaries and littoral wetlands throughout much of the United States. Life table response experiments (sensu Caswell 1989a) were carried out in the laboratory to compare the demographic responses of these species to three common sources of estuarine contamination or enrichment: sewage (Milorganite), blue-green algae (Spirulina sp.), and hydrocarbons (No. 2 fuel oil). Life table data were used to generate two population projection models (a fully age-classified model and a simple two-stage model) for each species in each treatment and in a salt marsh sediment control. These models were used to quantify the effects of treatments on survival, reproduction, and age at maturity, and hence on population growth rate. For both species, survival was high in all treatments except the blue-green algae treatment, where oxygen depletion (to <1 mL/L) occurred. Treatments had dramatic effects on age at maturity, fertility, and generation time, which differed between species and among contaminants. Population growth rates (X) were higher in Capitella sp. I than in S. benedicti for all treatments, primarily due to earlier maturation and a fertility advantage exhibited by Capitella during the first few weeks of reproduction. In Capitella sp. I, explosive increases in X were seen in the sewage (X = 5.31) and algae (X = 2.81) enrichments relative to the control (X = 1.86) and the hydrocarbon treatments (X = 1.67). Reduced maturation time and increases in age-specific fertility associated with rapid growth and large body size were responsible. Hydrocarbons reduced X primarily through delayed maturation and reduced age-specific fertility. Population growth rates of S. benedicti in the hydrocarbon treatment (X = 1.11) and algae treatment (X = 1.09) were reduced relative to the control (X = 1.46) and sewage treatments (X = 1.41). The hydrocarbon reduction resulted from delayed maturity and reduced fertility, whereas the algal effects were caused by reductions in both juvenile survival and fertility. Our analyses revealed that Capitella sp. Is population growth rate was less sensitive than that of S. benedicti to these three common forms of estuarine contamination, that different sources of organic enrichment (sewage and blue-green algae) introduced at the same C and N levels could have varying demographic effects, and that when two contaminants (hydrocarbons and blue-green algae) caused similar reductions in population growth rate in a species (Streblospio), the underlying mechanisms may have differed. For both species all demographically important effects of contaminants occurred early in life, suggesting a need to focus on juveniles and young adults in field and laboratory testing. The experiments performed here demonstrated the sensitivity of polychaete demo- graphic properties to the condition of estuarine sediments. This sensitivity may be exploited to evaluate organic enrichment and hydrocarbon contamination in field settings.

What Controls Connectivity? An Empirical, Multi-Species Approach

The exchange of individuals among habitat patches (connectivity) has broad relevance for the conservation and management of marine metapopulations. Elemental fingerprinting-based research conducted over the past 12 years along the open coastline and bays of San Diego County in southern California evaluated connectivity patterns for seven species: one native and two invasive mussels, an oyster, a brachyuran crab, and two fishes. The studies spanned different years and seasons but overlapped considerably in space, allowing comparisons of dispersal patterns across species, and assessment of the relative importance of location, circulation, and intra-annual and inter-annual variability. We asked whether the species exhibited commonalities in directional transport, transport distances, sources and sinks, self-recruitment, and bay-ocean exchange. Linked connectivity-demographic analyses conducted for two species of mytilid mussels and two fishes allowed evaluation of the contributions of realized connectivity to metapopulation dynamics relative to other life-history attributes. Common trends across species include average along-shore dispersal distances of 15-35 km and seasonal changes in direction of dispersal that mirrored patterns of along-shore circulation. We observed greater isolation of back-bay populations, significant exchange from front bay to ocean, and high self-recruitment in locations on the northern, open coast, and in the southern bays. Connectivity was rarely the most influential driver of growth and persistence of metapopulations, but influenced the importance of other vital rates. Several locations served consistently as sources of larvae or as nurseries for multiple species, but there were few sites in common that were sinks. For the mussels, reproductive timing guided directional transport. These results imply that local management (e.g., habitat protection, opening of the mouths of lagoons, location of aquaculture farms) may be effective along this coastline. Regional, multi-species assessments of exchange of larvae should move us closer to ecosystem-based management.

Relationship between propagule pressure and colonization pressure in invasion ecology: a test with ships' ballast

Increasing empirical evidence indicates the number of released individuals (i.e. propagule pressure) and number of released species (i.e. colonization pressure) are key determinants of the number of species that successfully invade new habitats. In view of these relationships, and the possibility that ships transport whole communities of organisms, we collected 333 ballast water and sediment samples to investigate the relationship between propagule and colonization pressure for a variety of diverse taxonomic groups (diatoms, dinoflagellates and invertebrates). We also reviewed the scientific literature to compare the number of species transported by ships to those reported in nature. Here, we show that even though ships transport nearly entire local communities, a strong relationship between propagule and colonization pressure exists only for dinoflagellates. Our study provides evidence that colonization pressure of invertebrates and diatoms may fluctuate widely irrespective of propagule pressure. We suggest that the lack of correspondence is explained by reduced uptake of invertebrates into the transport vector and the sensitivity of invertebrates and diatoms to selective pressures during transportation. Selection during transportation is initially evident through decreases in propagule pressure, followed by decreased colonization pressure in the most sensitive taxa.

Assessing the dispersal and exchange of brachyuran larvae between regions of San Diego Bay, California and nearshore coastal habitats using elemental fingerprinting

Marine benthic invertebrate populations found in estuarine or coastal habitats often exchange larvae. However, the dynamics of larval exchange are poorly understood because of difficulties in (1) making synoptic assessments of horizontal and vertical larval distribution patterns over large areas for extended periods of time and (2) determining the origins of field-sampled larvae. This study examines how temporal changes in the vertical and horizontal distribution of crab larvae (i.e., Pachygrapsus crassipes and Lophopanopeus spp.) affect larval transport. Larval concentration and water velocity data were collected concurrently and were used to estimate larval exchange between regions of San Diego Bay (SDB) and between SDB and nearshore coastal waters. A larval fingerprinting technique was used to distinguish SDB and non-SDB spawned, stage I P. crassipes zoeae to quantify larval exchange between SDB and nearshore coastal waters. First order estimates of larval exchange over a tidal cycle between inner and outer regions of SDB and between the bay and nearshore coastal habitats corroborate a net transport of stage I P crassipes zoeae from SDB as inferred from larval behavior. The estimated net larval exchange of Lophopanopeus spp. zoeae was into SDB, suggesting retention within the bay through larval development. Trace elemental fingerprinting of stage I P. crassipes zoeae revealed bi-directional exchange between SDB and the nearshore coastal environment when the predominant transport predicted from zoeal swimming behavior was out of San Diego Bay. Approximately 5% of stage I P crassipes zoeae sampled in the mid region of SDB originated from outside SDB, while 26% of zoeae sampled at the entrance originated from outside SDB. Combined use of trace elemental fingerprinting and synoptic field sampling techniques will help improve our understanding of larval transport and ultimately the population dynamics of nearshore species.

Connectivity Conservation: Connectivity in marine ecosystems: the importance of larval and spore dispersal

INTRODUCTION Connectivity is a concept shared in landscape and metapopulation ecology that is used to describe the movement or exchange of organisms between habitats on various temporal and spatial scales (Gilpin and Hanski 1991; Hanksi and Gilpin 1997; Crooks and Sanjayan Chapter 1; Taylor et al . Chapter 2; Moilanen and Hanski Chapter 3) and its population and community consequences. Many marine habitats, such as kelp forests, estuaries, wetlands, seagrass beds, coral and rocky reefs, and deep-sea hydrothermal vents, are naturally fragmented and patchy. As a result, many scientists working with marine populations and associated systems adopt a metapopulation-based interpretation of connectivity where landscapes are viewed as a network of habitat patches or fragments in which species occur as discrete local populations connected by the passive and active migration of individuals. In marine systems, connectivity may be generated by movements of early life stages such as larvae or spores (hereafter referred to as propagules), juveniles, or adults. The majority of marine organisms, including benthic (living on or in the bottom), demersal (living near and in close association with the bottom), and holoplanktonic (living in the plankton) species, have a complex life cycle characterized by planktonic stages of development (e.g., larvae, spores). In the case of marine invertebrates and fishes, propagules exhibit a diversity of nutritional modes, development sites, planktonic durations, and morphological development patterns that can affect patterns of connectivity (Table 8.1).

Identifying patterns of dispersal, connectivity and selection in the sea scallop, Placopecten magellanicus, using RADseq-derived SNPs

Understanding patterns of dispersal and connectivity among marine populations can directly inform fisheries conservation and management. Advances in high‐throughput sequencing offer new opportunities for estimating marine connectivity. We used restriction‐site‐associated DNA sequencing to examine dispersal and realized connectivity in the sea scallop Placopecten magellanicus, an economically important marine bivalve. Based on 245 individuals sampled rangewide at 12 locations from Newfoundland to the Mid‐Atlantic Bight, we identified and genotyped 7163 single nucleotide polymorphisms; 112 (1.6%) were identified as outliers potentially under directional selection. Bayesian clustering revealed a discontinuity between northern and southern samples, and latitudinal clines in allele frequencies were observed in 42.9% of the outlier loci and in 24.6% of neutral loci. Dispersal estimates derived using these clines and estimates of linkage disequilibrium imply limited dispersal; 373.1 ± 407.0 km (mean ± SD) for outlier loci and 641.0 ± 544.6 km (mean ± SD) for neutral loci. Our analysis suggests restricted dispersal compared to the species range (>2000 km) and that dispersal and effective connectivity differ. These observations support the hypothesis that limited effective dispersal structures scallop populations along eastern North America. These findings can help refine the appropriate scale of management and conservation in this commercially valuable species.

genepopedit: a simple and flexible tool for manipulating multilocus molecular data in R.

Advances in genetic sequencing technologies and techniques have made large, genome‐wide data sets comprised of hundreds or even thousands of individuals and loci the norm rather than the exception even for nonmodel organisms. While such data present new opportunities for evaluating population structure and demographic processes, the large size of these genomic data sets brings new computational challenges for researchers needing to parse, convert and manipulate data often into a variety of software‐specific formats required of genomic analyses. We developed genepopedit as a flexible tool for the manipulation of multilocus molecular data sets. Functionality can be divided among diagnostic‐, manipulation‐, sampling‐, simulation‐, and transformation‐based tools. Metadata from large genomic data sets can be efficiently extracted, without the need to view data in a text‐editing program. genepopedit provides tools to manipulate loci, individual samples and populations included in genomic data sets, in addition to the ability to convert directly to a variety of software formats. Functions are compiled as an R package, which can integrate into existing analysis workflows. Importantly, genepopedit provides a simple yet robust code‐based tool for repeatable genomic data manipulation, which has been proven to be stable for data sets in excess of 200 000 SNPs. The latest version of the package and associated documentation are available on Github (github.com/rystanley/genepopedit).

RAD sequencing reveals genomewide divergence between independent invasions of the European green crab (Carcinus maenas) in the Northwest Atlantic

Abstract Genomic studies of invasive species can reveal both invasive pathways and functional differences underpinning patterns of colonization success. The European green crab (Carcinus maenas) was initially introduced to eastern North America nearly 200 years ago where it expanded northwards to eastern Nova Scotia. A subsequent invasion to Nova Scotia from a northern European source allowed further range expansion, providing a unique opportunity to study the invasion genomics of a species with multiple invasions. Here, we use restriction‐site‐associated DNA sequencing‐derived SNPs to explore fine‐scale genomewide differentiation between these two invasions. We identified 9137 loci from green crab sampled from 11 locations along eastern North America and compared spatial variation to mitochondrial COI sequence variation used previously to characterize these invasions. Overall spatial divergence among invasions was high (pairwise FST ~0.001 to 0.15) and spread across many loci, with a mean FST ~0.052 and 52% of loci examined characterized by FST values >0.05. The majority of the most divergent loci (i.e., outliers, ~1.2%) displayed latitudinal clines in allele frequency highlighting extensive genomic divergence among the invasions. Discriminant analysis of principal components (both neutral and outlier loci) clearly resolved the two invasions spatially and was highly correlated with mitochondrial divergence. Our results reveal extensive cryptic intraspecific genomic diversity associated with differing patterns of colonization success and demonstrates clear utility for genomic approaches to delineating the distribution and colonization success of aquatic invasive species.

Swimming behavior and velocities of barnacle cyprids in a downwelling flume

It has been proposed that barnacle cyprids can maintain position in shoreward- propagating fronts by swimming upward against a downwelling flow, potentially mediating onshore transport of larvae toward intertidal habitat. This study developed a novel flume to characterize swimming behavior of barnacle cyprids in a laboratory downwelling flow. Seawater was pumped through a cylindrical observation chamber fitted with diffusers to produce a homogeneous down- welling velocity field. The flume generated plug flow with mean downwelling velocities (indicated by negative sign) of 0 to -47.3 mm s -1 . Behavior experiments were done with wild Semibalanus bal- anoides cyprids. Vertical swimming rates and behaviors were estimated from video observations, and a mixture model was used to estimate velocity distributions for distinct behavioral modes. Larvae exhibited multiple behaviors but typically swam upward in response to downwelling, with a maxi- mum estimated vertical velocity of 72.3 mm s -1 . When faced with downwelling flows, cyprids alter- nated between upward swimming and downward swimming to maintain their vertical position in the chamber. As downwelling velocities increased, cyprids that remained in the field of view of the cam- eras exhibited faster mean upward swimming velocities. It is unclear how long individual S. bal- anoides cyprids can maintain depth, but cyprids were able to maintain depth throughout the 2 min observation period. This study supports earlier hypotheses based on field observations by demon- strating that S. balanoides cyprids swim well enough to counter downwelling velocities characteris- tic of convergence zones. Swimming against downwelling flow could be an adaptive behavior that enables shoreward transport in the absence of any larval ability to swim toward shore or even to sense its direction.

Genomic evidence of hybridization between two independent invasions of European green crab ( Carcinus maenas ) in the Northwest Atlantic

Invasive species have been associated with significant negative impacts in their introduced range often outcompeting native species, yet the long-term evolutionary dynamics of biological invasions are not well understood. Hybridization, either among waves of invasion or between native and introduced populations, could alter the ecological and evolutionary impacts of invasions yet has rarely been studied in marine invasive species. The European green crab (Carcinus maenas) invaded eastern North America twice from northern and southern locations in its native range. Here we examine the frequency of hybridization among these two distinct invasions at locations from New Jersey, USA to Newfoundland, Canada using restriction-site-associated DNA sequencing (RAD-seq), microsatellite loci and cytochrome c oxidase subunit I mitochondrial DNA (mtDNA) sequences. We used Bayesian clustering and hybrid assignment analyses to investigate hybridization between the northern and southern populations. Of the samples analyzed, six locations contained at least one hybrid individual, while two locations were characterized by extensive hybridization, with 95% of individuals collected from Placentia Bay, Newfoundland being hybrids (mostly F2) and 90% of individuals from Kejimkujik, Nova Scotia being classified as hybrids, mostly backcrosses to the northern ecotype. The presence of both F2 hybrids and backcrossed individuals suggests that these hybrids are viable and introgression is occurring between invasions. Our results provide insight into the demographic and evolutionary consequences of hybridization between independent invasions, and will inform the management of green crabs in eastern North America.